The most important tools for RAW layers are the color adjustments — RAW images have additional color data so, for example, if an area is blown out (e.g. the highlights are completely white) you can recover it and bring back detail using the color adjustments. You can almost think of RAW images as layered images with lots of different color layers. That's probably not the best analogy, but I think the general idea behind it isn't entirely wrong. With that in mind, say you remove parts of an image using the Repair or Clone tools, all the other additional RAW data in the image wouldn't really make sense in this new image, which is why RAW layers need to be flattened before editing with particular tools. Maybe in the future, we can work out a way of keeping the RAW data with every tool you use, but for now, you'd need to do any color adjusting first, then retouching/reshaping afterward.